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In this work, molecular dynamics simulations are used to examine the self-assembly of anisotropically coated "patchy" nanoparticles. Specifically, we use a coarse-grained model to examine silica nanoparticles coated with alkane chains, where the poles of the grafted nanoparticle are bare, resulting in strongly attractive patches. Through a systematic screening process, the patchy nanoparticles are found to form dispersed, string-like, and aggregated phases, dependent on the combination of alkane chain length, coating chain density, and the fractional coated surface area. Correlation analysis is used to identify the ability of various particle descriptors to predict bulk phase behavior from more computationally efficient single grafted nanoparticle simulations and demonstrates that the solvent-accessible surface area of the nanoparticle core is a key predictor of bulk phase behavior. The results of this work enhance our knowledge of the phase space of patchy nanoparticles and provide a powerful approach for future screening of these materials. [ABSTRACT FROM AUTHOR]

The vapor-liquid equilibrium of binary mixtures of xenon + S[F.sub.6] was measured at nine temperatures from 235.34 to 295.79 K and pressure up to 6.5 MPa. The mixture critical line is continuous between the critical points of the pure components, hence the system is classified as type 1 phase behavior in the scheme of van Konynenburg and Scott.

Ab initio quantum chemical calculations were carried out to determine the structural properties as well as the intramolecular potentials for alkyl-substituted polyhedral oligomeric silsequioxane (POSS) macromolecules. The results indicated that the length of the linear hydrocarbon chain does not affect the structural or electronic properties of the POSS cage to which it is covalently bound.

An experimental and theoretical study of the thermodynamic properties of semifluorinated alkanes is performed. The results are interpreted using the SAFT-VR equation of state and the results are able to predict the thermodynamic behavior of the perfluoroalkylalkanes.

A charge-transfer reactive (CTR) force field along with other force fields taken from literature is used to predict the thermophysical properties of polyhedral oligomeric silsesquioxanes (POSS). All the force fields tested performed satisfactorily, but results indicate that the literature force field Hybrid-COMPASS and CTR predict structural properties of systems that contain POSS monomers, through molecular simulation.

The infinite dilution properties of two water +n-alkane mixtures by using a statistical associating fluid theory (SAFT) are presented. Recent theoretical and simulation studies suggest an unexpected shift in the solubility of n-alkanes in near critical water.

A study of the thermodynamic functions of the liquid mixtures xenon + n-butane and xenon + isobutane is presented. It is shown that the mixtures have a similar behavior to that of other xenon + alkane mixtures.

Measurements of total vapor pressures for liquid mixtures of xenon + propane at 161.40, 182.34 and 195.49 K and of xenone + ethane at 161.40 and 182.34 K reveal negative deviations from Raoult's law at all temperatures. The thermodynamics of the two liquid mixtures are further discussed.

The statistical associating fluid theory for chain molecules with attractive potentials for variable range was used to investigate the fluid-phase equilibria of the methane + n-hexane system. The system was found to exhibit a type V phase behavior, in which the two components display partial miscibility. The region of liquid-liquid immiscibility was accurately predicted by using the Lorentz-Berthelot mixing rules.

Grafting polymers to nanoparticles is one approach used to control and enhance the structure and properties of nanomaterials. However, predicting the aggregation behavior of tethered nanoparticles (TNPs) is a somewhat trial and error process as a result of the large number of possible polymer tethers, nanoparticles, and solvent species that can be studied. With the main goal of understanding how to control the dispersion and aggregation of TNP systems, molecular simulations and the hetero-statistical associating fluid theory for potentials of variable range have been used to calculate the fluid phase equilibrium of TNPs in both vacuum and in simple solvents under a wide range of conditions. The role of graft length, graft density, and solvent interactions is examined and trends established. Additionally, the fluid distribution ratio (k value) is used to study the solubility of TNPs in industrially relevant solvents including carbon dioxide, nitrogen, propane, and ethylene. [ABSTRACT FROM AUTHOR]

The fluid-solid phase transition behavior of nano-confined Lennard-Jones fluids as a function of temperature and degree of nanoconfinement has been studied via statistical temperature molecular dynamics (STMD). The STMD method allows the direct calculation of the density of states and thus the heat capacity with high efficiency. The fluids are simulated between parallel solid surfaces with varying pore sizes, wall-fluid interaction energies, and registry of the walls. The fluid-solid phase transition behavior has been characterized through determination of the heat capacity. The results show that for pores of ideal-spacing, the order-disorder transition temperature (TODT) is reduced as the pore size increases until values consistent with that seen in a bulk system. Also, as the interaction between the wall and fluid is reduced, TODT is reduced due to weak constraints from the wall. However, for non-ideal spacing pores, quite different behavior is obtained, e.g., generally TODT are largely reduced, and TODT is decreased as the wall constraint becomes larger. For unaligned walls (i.e., whose lattices are not in registry), the fluid-solid transition is also detected as T is reduced, indicating non-ideality in orientation of the walls does not impact the formation of a solid, but results in a slight change in TODT compared to the perfectly aligned systems. The STMD method is demonstrated to be a robust way for probing the phase transitions of nanoconfined fluids systematically, enabling the future examination of the phase transition behavior of more complex fluids. [ABSTRACT FROM AUTHOR]

The fluid-solid phase transition behavior of nano-confined Lennard-Jones fluids as a function of temperature and degree of nanoconfinement has been studied via statistical temperature molecular dynamics (STMD). The STMD method allows the direct calculation of the density of states and thus the heat capacity with high efficiency. The fluids are simulated between parallel solid surfaces with varying pore sizes, wall-fluid interaction energies, and registry of the walls. The fluid-solid phase transition behavior has been characterized through determination of the heat capacity. The results show that for pores of ideal-spacing, the order-disorder transition temperature (TODT) is reduced as the pore size increases until values consistent with that seen in a bulk system. Also, as the interaction between the wall and fluid is reduced, TODT is reduced due to weak constraints from the wall. However, for non-ideal spacing pores, quite different behavior is obtained, e.g., generally TODT are largely reduced, and TODT is decreased as the wall constraint becomes larger. For unaligned walls (i.e., whose lattices are not in registry), the fluid-solid transition is also detected as T is reduced, indicating non-ideality in orientation of the walls does not impact the formation of a solid, but results in a slight change in TODT compared to the perfectly aligned systems. The STMD method is demonstrated to be a robust way for probing the phase transitions of nanoconfined fluids systematically, enabling the future examination of the phase transition behavior of more complex fluids. [ABSTRACT FROM AUTHOR]

In this work, an extension is proposed to the standard iterative Boltzmann inversion (IBI) method used to derive coarse-grained potentials. It is shown that the inclusion of target data from multiple states yields a less state-dependent potential, and is thus better suited to simulate systems over a range of thermodynamic states than the standard IBI method. The inclusion of target data from multiple states forces the algorithm to sample regions of potential phase space that match the radial distribution function at multiple state points, thus producing a derived potential that is more representative of the underlying interactions. It is shown that the algorithm is able to converge to the true potential for a system where the underlying potential is known. It is also shown that potentials derived via the proposed method better predict the behavior of n-alkane chains than those derived via the standard IBI method. Additionally, through the examination of alkane monolayers, it is shown that the relative weight given to each state in the fitting procedure can impact bulk system properties, allowing the potentials to be further tuned in order to match the properties of reference atomistic and/or experimental systems. [ABSTRACT FROM AUTHOR]

Two different techniques - replica-exchange Wang-Landau (REWL) and statistical temperature molecular dynamics (STMD) - were applied to systematically study the phase transition behavior of self-assembling lipids as a function of temperature using an off-lattice lipid model. Both methods allow the direct calculation of the density of states with improved efficiency compared to the original Wang-Landau method. A 3-segment model of amphiphilic lipids solvated in water has been studied with varied particle interaction energies (&eh;) and lipid concentrations. The phase behavior of the lipid molecules with respect to bilayer formation has been characterized through the calculation of the heat capacity as a function of temperature, in addition to various order parameters and general visual inspection. The simulations conducted by both methods can go to very low temperatures with the whole system exhibiting well-ordered structures. With optimized parameters, several bilayer phases are observed within the temperature range studied, including gel phase bilayers with frozen water, mixed water (i.e., frozen and liquid water), and liquid water, and a more fluid bilayer with liquid water. The results obtained from both methods, STMD and REWL, are consistently in excellent agreement with each other, thereby validating both the methods and the results. [ABSTRACT FROM AUTHOR]

Systems composed of soft matter (e.g. liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges, requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation. Performing a molecular simulation of a soft matter system involves multiple steps, which have traditionally been performed by researchers in a 'bespoke' fashion, resulting in many published soft matter simulations not being reproducible based on the information provided in the publications. To address the issue of reproducibility and to provide tools for computational screening, we have been developing the open-source Molecular Simulation and Design Framework (MoSDeF) software suite. In this paper, we propose a set of principles to create Transparent, Reproducible, Usable by others, and Extensible (TRUE) molecular simulations. MoSDeF facilitates the publication and dissemination of TRUE simulations by automating many of the critical steps in molecular simulation, thus enhancing their reproducibilitya. We provide several examples of TRUE molecular simulations: All of the steps involved in creating, running and extracting properties from the simulations are distributed on open-source platforms (within MoSDeF and on GitHub), thus meeting the definition of TRUE simulations. [ABSTRACT FROM AUTHOR]

Configurational-bias Monte Carlo has been incorporated into the Wang-Landau method. Although the Wang-Landau algorithm enables the calculation of the complete density of states, its applicability to continuous molecular systems has been limited to simple models. With the inclusion of more advanced sampling techniques, such as configurational-bias, the Wang-Landau method can be used to simulate complex chemical systems. The accuracy and efficiency of the method is assessed using as a test case systems of linear alkanes represented by a united-atom model. With strict convergence criteria, the density of states derived from the Wang-Landau algorithm yields the correct heat capacity when compared to conventional Boltzmann sampling simulations. [ABSTRACT FROM AUTHOR]

The Wang-Landau (WL) Monte Carlo method has been applied to simulate the self-assembly of a lipid bilayer on a 3D lattice. The WL method differs from conventional Monte Carlo methods in that a complete density of states is obtained directly for the system, from which properties, such as the free energy, can be derived. Furthermore, from a single WL simulation, continuous curves of the average energy and heat capacity can be determined, which provide a complete picture of the phase behavior. The lipid model studied consists of 3 or 5 coarse-grained segments on lattices of varying sizes, with the empty lattice sites representing water. A bilayer structure is found to form at low temperatures, with phase transitions to clusters as temperature increases. For 3-segment chains, varying lattice sizes were studied, with the observation that the ratio of chain number to lattice area (i.e., area per lipid) affects the phase transition temperature. At small ratios, only one phase transition occurs between the bilayer and cluster phases, while at high lipid ratios the phase transition occurs in a two-step process with a stable intermediate phase. This second phase transition was not observed in conventional Metropolis Monte Carlo simulations on the same model, demonstrating the advantage of being able to perform a complete scan of the whole temperature range with the WL method. For longer 5-segment chains similar phase transitions are also observed with changes in temperature. In the WL method, due to the extensive nature of the energy, the number of energy bins required to represent the density of states increases as the system size increases and so limits its practical application to larger systems. To improve this, an extension of the WL algorithm, the statistical-temperature Monte Carlo method that allows simulations with larger energy bin sizes, has recently been proposed and is implemented in this work for the 3-segment lattice model. The results obtained are in good agreement with the original WL method and appear to be independent of the energy bin size used. [ABSTRACT FROM AUTHOR]

We present a Fourier space density functional approach for hard particles with attractive interactions, which is based on a previously developed two-dimensional approach [S. Hlushak, W. Rżysko, and S. Sokołowski, J. Chem. Phys. 131, 094904 (2009)] for hard-sphere chains. The interactions are incorporated by means of a three-dimensional Fourier image of the direct correlation function that is obtained from the first-order mean-spherical approximation. In order to improve the computational efficiency, we make extensive use of fast Fourier transforms for calculating density convolution integrals. A two-dimensional implementation of the new density functional approach, based on the expansion of the functional around the bulk fluid density, is used to study structure and adsorption of two model fluids in narrow cylindrical pores. We also investigate two methods that improve the accuracy of the theory as compared to the conventional DFT approach, which expands the free energy functional around the bulk fluid density: One a variant of the reference fluid density functional theory used by Gillespie et al. [Phys. Rev. E 68, 031503 (2003)], and the second a weighted density approach with energy route thermodynamics. Results from these two methods are compared to the conventional approach and also to the results of Monte Carlo simulations. We find that the method of Gillespie et al. and the weighted density approach with energy route thermodynamics yield significant improvement over the conventional approach. [ABSTRACT FROM AUTHOR]

Monolayers presenting methyl-terminated (hydrophobic) and hydroxyl-terminated (hydrophilic) surfaces on silica have been studied by molecular dynamics simulation and the effects of hydrogen bonding, chain length, and chain mixing on the frictional properties determined. The hydroxyl-terminated monolayers were found to show large adhesion zones as a result of strong interfacial interlayer hydrogen bonds; the interfacial sliding forces observed in the hydroxyl-terminated monolayers being one order of magnitude higher than the interfacial forces for the hydrophobic surfaces at the characteristic point of zero-load. Mixed hydroxyl- and methyl-terminated monolayers of equal length were found to exhibit intermediate shear stress values between those observed for pure monolayers, with the magnitude of the shear stress depending on the surface content of the hydroxyl-terminated chains. For mixed monolayers of unequal chain lengths, at high loads a maximum in the magnitude of the shear stress as a function of the length of the methyl-terminated chain was observed due to the creation of a buffer zone between the hydroxyl-terminated chains that produces strong hydrogen-bonding interactions. The effect of a constant normal load or constant separation simulation ensemble on the results has also been studied and in general found to have minimal influence on the observed behavior, although some differences are observed for the shear stress at intermediate normal loads due to the formation of stronger hydrogen bond networks at constant load compared to constant separation. [ABSTRACT FROM AUTHOR]

A coarse-grained model has been developed for simulating the self-assembly of nonyl-tethered polyhedral oligomeric silsesquioxane (POSS) nanoparticles in solution. A mapping scheme for groups of atoms in the atomistic molecule onto beads in the coarse-grained model was established. The coarse-grained force field consists of solvent-mediated effective interaction potentials that were derived via a structural-based coarse-graining numerical iteration scheme. The force field was obtained from initial guesses that were refined through two different iteration algorithms. The coarse-graining scheme was validated by comparing the aggregation of POSS molecules observed in simulations of the coarse-grained model to that observed in all-atom simulations containing explicit solvent. At 300 K the effective coarse-grained potentials obtained from different initial guesses are comparable to each other. At 400 K the differences between the force fields obtained from different initial guesses, although small, are noticeable. The use of a different iteration algorithm employing identical initial guesses resulted in the same overall effective potentials for bare cube corner bead sites. In both the coarse-grained and all-atom simulations, small aggregates of POSS molecules were observed with similar local packings of the silsesquioxane cages and tether conformations. The coarse-grained model afforded a savings in computing time of roughly two orders of magnitude. Further comparisons were made between the coarse-grained monotethered POSS model developed here and a minimal model developed in earlier work. The results suggest that the interactions between POSS cages are long ranged and are captured by the coarse-grained model developed here. The minimal model is suitable for capturing the local intermolecular packing of POSS cubes at short separation distances. [ABSTRACT FROM AUTHOR]

The statistical associating fluid theory for potentials of variable range plus dipole (SAFT-VR+D) is extended to study associating dipolar fluids. In the SAFT-VR+D approach dipolar interactions are taken into account through the use of the generalized mean spherical approximation to describe a reference fluid of dipolar square-well segments. This enables the effect of the dipolar interactions on the thermodynamics and structure of fluids to be explicitly described. Predictions for the thermodynamic properties and phase behavior of dipolar associating square-well monomers with one, two, and four association sites are considered and compared with new isothermal-isobaric and Gibbs ensemble Monte Carlo simulation data. The results show that the SAFT-VR+D equation provides a good description of the phase behavior of dipolar associating fluids. Additionally we have applied the new theoretical approach to study the vapor pressure and saturated liquid density of water. [ABSTRACT FROM AUTHOR]

A statistical associating fluid theory to model electrolyte fluids that explicitly accounts for solvent molecules by modeling water as a dipolar square-well associating fluid is presented. Specifically the statistical associating fluid theory for potentials of variable range (SAFT-VR) is combined with integral equation theory and the generalized mean spherical approximation using the nonprimitive model to describe the long-range ion-ion, ion-dipole, and dipole-dipole interactions. Isothermal-isobaric ensemble Monte Carlo simulations have been performed in order to test the new theoretical approach. In particular, simulations are performed for different ion concentrations and different ratios of the cation, anion, and solvent segment diameters. Predictions for the thermodynamic properties from the new equation of state are compared with the computer simulation data. Additionally, results from a combination of the SAFT-VR approach with Debye-Hückel theory and the primitive model are also presented and compared to those obtained with the nonprimitive model to illustrate the advantages of the new statistical associating fluid theory for potentials of variable range plus dipole and electrolytes (SAFT-VR+DE) approach. The results show that the proposed equation of state provides a good description of the PVT properties of electrolyte fluids with different sizes of ions and solvent. [ABSTRACT FROM AUTHOR]

A molecular thermodynamics approach is developed in order to describe the adsorption of fluids on solid surfaces. The new theory is based on the statistical associating fluid theory for potentials of variable range [A. Gil-Villegas et al., J. Chem. Phys. 106, 4168 (1997)] and uses a quasi-two-dimensional approximation to describe the properties of adsorbed fluids. The theory is tested against Gibbs ensemble Monte Carlo simulations and excellent agreement with the theoretical predictions is achieved. Additionally the authors use the new approach to describe the adsorption isotherms for nitrogen and methane on dry activated carbon. [ABSTRACT FROM AUTHOR]

Nonequilibrium molecular dynamics (NEMD) simulations were performed and the transient time correlation function (TTCF) method applied to calculate the shear viscosity of n-decane. Using the TTCF method we were able to calculate the viscosity at shear rate orders of magnitude lower than is possible by direct NEMD simulation alone. For the first time for a molecular fluid, we were able to simulate shear rates accessible by experimental measurements, which are typically performed at shear rates well below those accessible by NEMD simulation. The TTCF method allows us to close the gap between the lowest shear rates accessible by MD simulation and the highest shear rates possible in experimental studies. Additionally a multiple time step method for Gaussian thermostatted SLLOD equations of motion was developed following earlier work [G. A. Pan et al., J. Chem. Phys. 122, 4114 (2005)] for atomic fluids. [ABSTRACT FROM AUTHOR]

A statistical associating fluid theory for potentials of variable range to model dipolar fluids is presented. The new theory, termed the SAFT-VR+D equation (the statistical associating fluid theory for potentials of variable range plus dipole), explicitly accounts for dipolar interactions and their effect on the structure of the fluid. This is achieved through the use of the generalized mean spherical approximation (GMSA) to describe a reference fluid of dipolar square-well segments. Isothermal-isobaric and Gibbs ensemble Monte Carlo simulations have been performed in order to test the new theoretical approach. Predictions for the thermodynamic properties and phase behavior of dipolar square-well monomer and chain fluids, in which one or more segments are dipolar, are considered and compared with new computer simulation data. The results show that the equation of state in general provides a good description of the phase behavior of dipolar monomer and chain fluids. Some deviations are seen between the simulation data and theoretical predictions for monomer fluids with large dipole moments and for molecules composed of segments with dipoles in different orientations. This is addressed through the replacement of the GMSA by the linearized exponential approximation. [ABSTRACT FROM AUTHOR]

We report molecular dynamics simulations for telechelic molecules composed of two polyhedral oligomeric silsesquioxane (POSS) cages connected by one hydrocarbon backbone dissolved in liquid normal hexane. Silsesquioxanes are novel hybrid organic-inorganic molecules that are useful as building blocks for the synthesis of nanostructured materials. By including POSS molecules within a polymeric material it is possible to modify mechanical properties such as resistance to heat and glass transition temperatures. Unfortunately, the molecular mechanisms responsible for these enhancements are at present not completely understood. In an effort to elucidate the molecular phenomena responsible for these effects, we have studied the conformation of telechelic POSS molecules in solution, as well as their self-diffusion coefficients, as a function of the length of the hydrocarbon backbone. We focus on molecules in which the radius of gyration of the alkane backbone is comparable to the size of the silsesquioxane cages. Our results indicate that the backbone has a significant influence on both the equilibrium and the transport properties of dissolved telechelic hybrid molecules. These observations are useful for developing strategies to direct the self-assembly of nanostructured materials. [ABSTRACT FROM AUTHOR]

We apply an operator splitting method to develop a simulation algorithm that has complete analytical solutions for the Gaussian thermostated SLLOD equations of motion [D. J. Evans and G. P. Morriss, Phys. Rev. A 30, 1528 (1984)] for a system under shear. This leads to a homogeneous algorithm for performing both equilibrium and nonequilibrium isokinetic molecular dynamics simulation. The resulting algorithm is computationally efficient. In particular, larger integration time steps can be used compared to simulations with regular Gaussian thermostated SLLOD equations of motion. The utility and accuracy of the algorithm are demonstrated through application to the Weeks–Chandler–Anderson fluid. Although strict conservation of the kinetic energy suppresses thermal fluctuations in the system, this algorithm does not allow simulations at lower shear rates than those normally afforded by older nonequilibrium molecular dynamics simulations. [ABSTRACT FROM AUTHOR]

The accuracy of several theories for the thermodynamic properties of the Yukawa hard-sphere chain fluid are studied. In particular, we consider the polymer mean spherical approximation (PMSA), the dimer version of thermodynamic perturbation theory (TPTD), and the statistical associating fluid theory for potentials of variable attractive range (SAFT-VR). Since the original version of SAFT-VR for Yukawa fluids is restricted to the case of one-Yukawa tail, we have extended SAFT-VR to treat chain fluids with two-Yukawa tails. The predictions of these theories are compared with Monte Carlo (MC) simulation data for the pressure and phase behavior of the chain fluid of different length with one- and two-Yukawa tails. We find that overall the PMSA and TPTD give more accurate predictions than SAFT-VR, and that the PMSA is slightly more accurate than TPTD. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The prediction of viscosity by molecular simulation has been a goal of molecular modeling essentially since its inception. With today's computing power, the Newtonian or zero shear viscosity of a low molecular weight fluid can easily be determined using equilibrium and nonequilibrium molecular dynamics simulation methods. However, both methods are constrained to systems with relatively short relaxation times that are accessible on the timescale of a molecular dynamics simulation. Here we demonstrate that using a simple scaling relation enables us to predict the Newtonian viscosity of a molecule at any state point for a small fraction of the time that it takes to obtain the same result through nonequilibrium or equilibrium molecular dynamics simulation. [ABSTRACT FROM AUTHOR]

A statistical associating fluid theory for potential of variable range is developed to model dipolar fluids (SAFT-VR+D) and the high-pressure phase diagram of hydrogen sulfide + n-alkane binary mixtures is examined. The SAFT-VR+D theory has explored and predicted the effect of temperature and the molecular weight of the hydrocarbon component on the solubility of [H.sub.2]S in the n-alkanes.